Using a silo structure to send link juice through your site is a great way to improve your site’s Panda Score and also help you with long-tail rankings.
By sending high PR links to your home page and then linking internally in a silo fashion you can send large amounts of link juice to internal pages.
High PR Links
As long as you have set up your site in a silo structure you can use your very best high PageRank links to link to your root domain and start the flow of link juice moving throughout your site.
If you are trying to rank your homepage for a specific term then you should use your EMK (exact match keywords) in your high PR link anchors – as long as you observe the proper anchor text ratios!
If you are trying to build your authority then use brand terms, your naked URL and market/niche specific keywords instead.
This relevant high PR link juice will then begin to flow through all your pages building the authority of your entire web site and also helping to rank your other pages.
Long Tail Ranking
By silo-ing your site and sending high PR links to your homepage you can then create internal pages optimized for easier to rank long-tail keywords and have link juice sent to them automatically.
Many times this strategy alone is enough to get a page optimized for a long-tail keyword to rank on the first page of Google.